3EE9 - JenaLib

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Title :   STRUCTURE OF NS1 EFFECTOR DOMAIN

Authors :   S. Xia, A. F. Monzingo, J. D. Robertus

Date :   04 Sep 08 (Deposition) - 13 Jan 09 (Release) - 05 Jan 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.14

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Zinc Finger Receptor, Alternative Splicing, Cytoplasm, Host- Virus Interaction, Interferon Antiviral System Evasion, Nucleus, Rna-Binding, Suppressor Of Rna Silencing, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Xia, A. F. Monzingo, J. D. Robertus
Structure Of Ns1A Effector Domain From The Influenza A/Udorn/72 Virus.
Acta Crystallogr. , Sect. D V. 65 11 2009
PubMed-ID: 19153461 | Reference-DOI: 10.1107/S0907444908032186
(for further references see the PDB file header)

Molecule 1 - NON-STRUCTURAL PROTEIN 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET46
	Expression System Strain	:	ROSETTA 2
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	EFFECTOR DOMAIN (UNP RESIDUES 84-205)
	Gene	:	NS
	Organism Scientific	:	INFLUENZA A VIRUS (A/UDORN/307/1972(H3N2))
	Organism Taxid	:	381517
	Strain	:	UDORN
	Synonym	:	NS1, NS1A

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:193 , GLN A:199 , HOH A:230 , HOH A:259	BINDING SITE FOR RESIDUE SO4 A 1
2	AC2	SOFTWARE	ARG B:193 , LYS B:196 , GLN B:199 , HOH B:237	BINDING SITE FOR RESIDUE SO4 B 2

(no "SS Bond" information available for 3EE9)

(no "Cis Peptide Bond" information available for 3EE9)

(no "SAP(SNP)/Variant" information available for 3EE9)

(no "PROSITE Motif" information available for 3EE9)

(no "Exon" information available for 3EE9)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:122
 aligned with NS1_I72A2 | P03495 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:122
                                    93       103       113       123       133       143       153       163       173       183       193       203  
            NS1_I72A2    84 TPASRYITDMTIEELSRDWFMLMPKQKVEGPLCIRIDQAIMDKNIMLKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSFPGHTIEDVKNAIGVLIGGLEWNDNTVRVSKTLQRFAWGS 205
               SCOP domains d3ee9a_ A: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhh.eee..hhhhhhh......eeeeee..eeeeee......eeeeeeeeeee..eeeeeeeeeeee....eeeeeee.......hhhhhhhhhhhhhhhhhhh..eeeehhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ee9 A  84 TPASRYITDMTIEELSRDWFMLMPKQKVEGPLCIRIDQAIMDKNIMLKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSFPGHTIEDVKNAIGVLIGGLEWNDNTVRVSKTLQRFAWGS 205
                                    93       103       113       123       133       143       153       163       173       183       193       203

Chain B from PDB  Type:PROTEIN  Length:118
 aligned with NS1_I72A2 | P03495 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:118
                                    96       106       116       126       136       146       156       166       176       186       196        
            NS1_I72A2    87 SRYITDMTIEELSRDWFMLMPKQKVEGPLCIRIDQAIMDKNIMLKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSFPGHTIEDVKNAIGVLIGGLEWNDNTVRVSKTLQRFAWG 204
               SCOP domains d3ee9b_ B: automated matches                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..hhhhhhh......eeeeee..eeeeee......eeeeeeeeeee..eeeeeeeeeee.....eeeeeee.......hhhhhhhhhhhhhhhhhhh..eeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3ee9 B  87 SRYITDMTIEELSRDWFMLMPKQKVEGPLCIRIDQAIMDKNIMLKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSFPGHTIEDVKNAIGVLIGGLEWNDNTVRVSKTLQRFAWG 204
                                    96       106       116       126       136       146       156       166       176       186       196

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Ns1 effector domain-like (19)

Superfamily: Ns1 effector domain-like (19)

Family: Ns1 effector domain-like (19)

Protein domain: automated matches (18)

Influenza a virus (a/udorn/307/1972(h3n2)) [TaxId: 381517] (2)

1a	d3ee9a_	A:
1b	d3ee9b_	B:

(no "CATH Domain" information available for 3EE9)

(no "Pfam Domain" information available for 3EE9)

Asymmetric Unit(hide GO term definitions)

Chain A,B (NS1_I72A2 | P03495)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003725	double-stranded RNA binding	Interacting selectively and non-covalently with double-stranded RNA.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0030683	evasion or tolerance by virus of host immune response	Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0052038	modulation by symbiont of host intracellular transport	Any process in which an organism modulates the frequency, rate or extent of the directed movement of substances within the cell or cells of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0019056	modulation by virus of host transcription	Any process in which a virus modulates the frequency, rate or extent of its host's transcription.
	GO:0052170	negative regulation by symbiont of host innate immune response	Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of the innate immune response of the host organism, the host's first line of defense against infection. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0039580	suppression by virus of host PKR activity	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host PKR (protein kinase regulated by RNA) activity. Activation of PKR involves dsRNA binding followed by autophosphorylation. Phosphorylated PKR can then phosphorylate downstream targets such as the translation initiation factor eIF2 to inhibit protein synthesis. Viruses encode a number of mechanisms to inhibit the host antiviral response via PKR, including direct interaction with PKR, promoting degradation of PKR or altering the subcellular location of PKR.
	GO:0039540	suppression by virus of host RIG-I activity	Any process in which a virus stops, prevents, or reduces the activity of RIG-1 (also known as DDX58). The cytoplasmic pattern recognition RIG-I recognizes viral RNA synthesized during active viral replication and signals to protect the host against viral infection, for example by inducing the expression of antiviral cytokines.
	GO:0046775	suppression by virus of host cytokine production	Any viral process that results in the inhibition of host cell cytokine production.
	GO:0039657	suppression by virus of host gene expression	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of gene expression in the host organism. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
	GO:0039503	suppression by virus of host innate immune response	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the innate immune response of the host organism, the host's first line of defense.
	GO:0039524	suppression by virus of host mRNA processing	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of mRNA processing in the host cell. mRNA processing is the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
	GO:0039502	suppression by virus of host type I interferon-mediated signaling pathway	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of type I interferon-mediated signaling in the host organism. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0030430	host cell cytoplasm	The cytoplasm of a host cell.
	GO:0042025	host cell nucleus	A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.

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	NS1_I72A2 \| P03495	:	1ail 1ns1 2kkz 2rhk 3ee8 3kwg 3kwi 4nw2 4o45

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